Tag: statistics

Rhinology. 2022 Oct 27. doi: 10.4193/Rhin22.176. Online ahead of print.

ABSTRACT

BACKGROUND: Chemosensory dysfunction (CD) has been reported as a common symptom of SARS-CoV-2 infection, but it is not well understood whether and for how long changes of smell, taste and chemesthesis persist in infected individuals.

METHODOLOGY: Unselected adult residents of the German federal state of Schleswig-Holstein with Polymerase Chain Reaction (PCR)-test-confirmed SARS-CoV-2 infection were invited to participate in this large cross-sectional study. Data on the medical history and subjective chemosensory function of participants were obtained through questionnaires and visual analogue scales (VAS). Olfactory function (OF) was objectified with the Sniffin’ Sticks test (SST), including threshold (T), discrimination (D) and identification (I) test as well as summarized TDI score, and compared to that in healthy controls. Gustatory function (GF) was evaluated with the suprathreshold taste strips (TS) test, and trigeminal function was tested with an ampoule containing ammonia.

RESULTS: Between November 2020 and June 2021, 667 infected individuals (mean age: 48.2 years) were examined 9.1 months, on average, after positive PCR testing. Of these, 45.6% had persisting subjective olfactory dysfunction (OD), 36.2% had subjective gustatory dysfunction (GD). Tested OD, tested GD and impaired trigeminal function were observed in 34.6%, 7.3% and 1.8% of participants, respectively. The mean TDI score of participants was significantly lower compared to healthy subjects. Significant associations were observed between subjective OD and GD, and between tested OD and GD.

CONCLUSION: Nine months after SARS-CoV-2 infection, OD prevalence is significantly increased among infected members of the general population. Therefore, OD should be included in the list of symptoms collectively defining Long-COVID.

PMID:36323438 | DOI:10.4193/Rhin22.176

J Immunol. 2022 Nov 2:ji2200366. doi: 10.4049/jimmunol.2200366. Online ahead of print.

ABSTRACT

Dendritic cells (DCs) are functionally diverse and are present in most adult tissues, but deep understanding of human DC biology is hampered by relatively small numbers of these in circulation and their short lifespan in human tissues. We built a transcriptional atlas of human DCs by combining samples from 14 expression profiling studies derived from 10 laboratories. We identified significant gene expression variation of DC subset-defining markers across tissue type and upon viral or bacterial stimulation. We further highlight critical gaps between in vitro-derived DC subsets and their in vivo counterparts and provide evidence that monocytes or cord blood progenitor in vitro-differentiated DCs fail to capture the repertoire of primary DC subsets or behaviors. In constructing a reference DC atlas, we provide an important resource for the community wishing to identify and annotate tissue-specific DC subsets from single-cell datasets, or benchmark new in vitro models of DC biology.

PMID:36323411 | DOI:10.4049/jimmunol.2200366

Clin Transplant. 2022 Nov 2:e14846. doi: 10.1111/ctr.14846. Online ahead of print.

ABSTRACT

We aimed to assess the effect of donor pancreas extraction time (ET) on postoperative complications and graft function after pancreas transplantation (PT). We analyzed all consecutive donor pancreas procurements for the simultaneous pancreas and kidney transplantation (SPK) and the associated PT in a Swiss transplant center over a 20-year period. Pancreas ET was defined as the time from cold flush to static storage of the pancreas on ice. The primary endpoint was the effect of extraction time on surgical complications. Secondary endpoints comprised the effect of ET on graft function (insulin-free survival) and graft pancreatitis. Of 115 procured pancreas grafts the median donor pancreas ET was 65 min (IQR: 48-78 min). In multivariable analysis, ET did not negatively affect major complications (OR 1.41 [95% CI: .59-3.36]; p = .438) and insulin-free survival (HR 1.42 [95% CI: .55-3.63]; p = .459). The median CIT was 522 (441-608) min. CIT was associated with major complications (OR 2.51 [95% CI: 1.11-5.68]; p = .027), but without impact on insulin-free survival (HR 1.94 [95% CI: .84-4.48]; p = .119). Patients with and without graft pancreatitis had no statistically significant differences in ET and CIT (p = .164 and p = .47, respectively). In multivariable analysis, Amylase levels > 270 U/L on postoperative day 1 were significantly associated with major complications (OR 3.61 [95% CI: 1.06-12.32]; p = .040). Our results suggest that although no effect of ET on complications and graft function after PT was found, shorter CIT and less graft pancreatitis can have a positive impact on surgical complications. Results could possibly be influenced by the exceptional quality of the pancreas donors, with short travel distances and preservation times in Switzerland. This article is protected by copyright. All rights reserved.

PMID:36322914 | DOI:10.1111/ctr.14846

J Comput Biol. 2022 Nov 2. doi: 10.1089/cmb.2022.0394. Online ahead of print.

ABSTRACT

ABSTRACT The accurate detection of point mutations from pathology slides using sequencing data is of great importance in cancer genomics and precision oncology. Formalin-fixation paraffin-embedding (FFPE) is a widely used technique to preserve pathology tissues. The FFPE process introduces artificial C > T mutations in next-generation sequencing, so we set out to develop excerno, a method to score and filter such spurious variants. FFPE mutational artifacts follow a mutational signature. By using the FFPE signature and Bayes’ formula, we can calculate the probability of a mutation resulting from the FFPE process and use this probability to filter FFPE variants. We implement this method as the excerno R package. We tested excerno by simulating mutations across all 60-baseline mutational signatures from the Catalog of Somatic Mutations in Cancer (COSMIC) and combining them with mutations following the FFPE mutational signature. The sensitivity and specificity of excerno are adversely affected by the cosine similarity between the baseline and FFPE signatures ($co{s}_{FFPE}$). Higher percentages of FFPE mutations ($pc{t}_{FFPE}$) result in increased sensitivity and reduced specificity. The specificity and sensitivity of excerno can be predicted as linear model with an interaction term using $co{s}_{FFPE}$and $pc{t}_{FFPE}$, with an $R^{2}of0.84$and 0.79, respectively. Finally, we tested excerno using six RNA sequencing cancer samples and observed concordant trends of specificity and sensitivity with respect to our simulated data. The excerno R package can be used to annotate and filter FFPE-induced mutations in cancer genomics. Our method is adversely affected by $co{s}_{FFPE}$and $pc{t}_{FFPE}$.

PMID:36322906 | DOI:10.1089/cmb.2022.0394

J Clin Oncol. 2022 Nov 2:JCO2200699. doi: 10.1200/JCO.22.00699. Online ahead of print.

ABSTRACT

PURPOSE: Fear of cancer recurrence (FCR) is a common distressing condition. We investigated the efficacy of smartphone problem-solving therapy and behavioral activation applications in breast cancer survivors.

METHODS: This was a decentralized randomized trial. Participants were disease-free breast cancer survivors age 20-49 years who were randomly assigned to the smartphone-based intervention or waitlist control. Both groups received treatment as usual. The control group could access the smartphone apps during weeks 8-24. The intervention comprised smartphone problem-solving therapy and behavioral activation apps. The primary end point was the Concerns About Recurrence Scale at week 8. Secondary outcomes included the Fear of Cancer Recurrence Inventory-Short Form (FCRI-SF), the Hospital Anxiety and Depression Scale (HADS), the Short-form Supportive Care Needs Survey (SCNS-SF34), and the Posttraumatic Growth Inventory at weeks 8 and 24 (trial registration: UMIN-CTR: UMIN000031140).

RESULTS: The intervention group included 223 participants, and the control group included 224 participants. Primary outcome data were obtained for 444 participants, and 213 participants in the intervention arm completed the week 24 assessment. The intervention group had statistically greater improvements than controls at week 8 on the Concerns About Recurrence Scale (difference -1.39; 95% CI, -1.93 to -0.85; P < .001), FCRI-SF (difference -1.65; 95% CI, -2.41 to -0.89; P < .001), HADS depression (difference -0.49; 95% CI, -0.98 to 0; P < .05), and SCNS-SF34 psychological domain (difference -1.49; 95% CI, -2.67 to -0.32; P < .05). These scores at week 24 were not statistically significant compared with week 8 although the HADS depression score at week 24 was significantly reduced (P = .03).

CONCLUSION: Novel smartphone psychotherapy offers a promising way to reduce FCR given the large number of survivors and a limited number of therapists to competently conduct psychotherapy.

PMID:36322882 | DOI:10.1200/JCO.22.00699

N Engl J Med. 2022 Nov 3;387(18):1661-1672. doi: 10.1056/NEJMoa2204886.

ABSTRACT

BACKGROUND: Whether higher parenteral amino acid intake improves outcomes in infants with extremely low birth weight is unclear.

METHODS: In this multicenter, parallel-group, double-blind, randomized, placebo-controlled trial, we assigned infants with birth weights of less than 1000 g at 8 neonatal intensive care units to receive amino acids at a dose of 1 g per day (intervention group) or placebo in addition to usual nutrition for the first 5 days after birth. The primary outcome was survival free from neurodisability as assessed with the Bayley Scales of Infant and Toddler Development and neurologic examination at 2 years, corrected for gestational age at birth. Secondary outcomes were the components of the primary outcome as well as the presence or absence of neonatal disorders, the rate of growth, and nutritional intake.

RESULTS: We enrolled 434 infants (217 per group) in this trial. Survival free from neurodisability was observed in 97 of 203 children (47.8%) in the intervention group and in 102 of 205 (49.8%) in the placebo group (adjusted relative risk, 0.95; 95% confidence interval [CI], 0.79 to 1.14; P = 0.56). Death before the age of 2 years occurred in 39 of 217 children (18.0%) in the intervention group and 42 of 217 (19.4%) in the placebo group (adjusted relative risk, 0.93; 95% CI, 0.63 to 1.36); neurodisability occurred in 67 of 164 children (40.9%) in the intervention group and 61 of 163 (37.4%) in the placebo group (adjusted relative risk, 1.16; 95% CI, 0.90 to 1.50). Neurodisability was moderate to severe in 27 children (16.5%) in the intervention group and 14 (8.6%) in the placebo group (adjusted relative risk, 1.95; 95% CI, 1.09 to 3.48). More children in the intervention group than in the placebo group had patent ductus arteriosus (adjusted relative risk, 1.65; 95% CI, 1.11 to 2.46). In a post hoc analysis, refeeding syndrome occurred in 42 of 172 children in the intervention group and 26 of 166 in the placebo group (adjusted relative risk, 1.64; 95% CI, 1.09 to 2.47). Eight serious adverse events occurred.

CONCLUSIONS: In infants with extremely low birth weight, extra parenteral amino acids at a dose of 1 g per day for 5 days after birth did not increase the number who survived free from neurodisability at 2 years. (Funded by the New Zealand Health Research Council and others; ProVIDe Australian New Zealand Clinical Trials Registry number, ACTRN12612001084875.).

PMID:36322845 | DOI:10.1056/NEJMoa2204886

N Engl J Med. 2022 Nov 3;387(18):1649-1660. doi: 10.1056/NEJMoa2206660.

ABSTRACT

BACKGROUND: In adults with advanced-stage Hodgkin’s lymphoma, the CD30-directed antibody-drug conjugate brentuximab vedotin combined with multiagent chemotherapy has been shown to have greater efficacy, but also more toxic effects, than chemotherapy alone. The efficacy of this targeted therapy approach in children and adolescents with Hodgkin’s lymphoma is unclear.

METHODS: We conducted an open-label, multicenter, randomized, phase 3 trial involving patients 2 to 21 years of age with previously untreated Hodgkin’s lymphoma of stage IIB with bulk tumor or stage IIIB, IVA, or IVB. Patients were assigned to receive five 21-day cycles of brentuximab vedotin with doxorubicin, vincristine, etoposide, prednisone, and cyclophosphamide (brentuximab vedotin group) or the standard pediatric regimen of doxorubicin, bleomycin, vincristine, etoposide, prednisone, and cyclophosphamide (standard-care group). Slow-responding lesions, defined by a score of 4 or 5 (on a 5-point scale, with scores of 1 to 3 indicating rapid-responding lesions), were identified on centrally reviewed positron-emission tomography-computed tomography after two cycles. Involved-site radiation therapy was administered after the fifth cycle of therapy to slow-responding lesions and to large mediastinal adenopathy that was present at diagnosis. The primary end point was event-free survival, defined as the time until disease progression occurred, relapse occurred, a second malignant neoplasm developed, or the patient died. Safety and overall survival were assessed.

RESULTS: Of 600 patients who were enrolled across 153 institutions, 587 were eligible. At a median follow-up of 42.1 months (range, 0.1 to 80.9), the 3-year event-free survival was 92.1% (95% confidence interval [CI], 88.4 to 94.7) in the brentuximab vedotin group, as compared with 82.5% (95% CI, 77.4 to 86.5) in the standard-care group (hazard ratio for event or death, 0.41; 95% CI, 0.25 to 0.67; P<0.001). The percentage of patients who received involved-site radiation therapy did not differ substantially between the brentuximab vedotin group and the standard-care group (53.4% and 56.8%, respectively). Toxic effects were similar in the two groups. Overall survival at 3 years was 99.3% (95% CI, 97.3 to 99.8) in the brentuximab vedotin group and 98.5% (95% CI, 96.0 to 99.4) in the standard-care group.

CONCLUSIONS: The addition of brentuximab vedotin to standard chemotherapy resulted in superior efficacy, with a 59% lower risk of an event or death, and no increase in the incidence of toxic effects at 3 years. (Funded by the National Institutes of Health and others; AHOD1331 ClinicalTrials.gov number, NCT02166463.).

PMID:36322844 | DOI:10.1056/NEJMoa2206660

N Engl J Med. 2022 Nov 2. doi: 10.1056/NEJMoa2210058. Online ahead of print.

ABSTRACT

BACKGROUND: The BNT162b2 vaccine against coronavirus disease 2019 (Covid-19) has been authorized for use in children 5 to 11 years of age and adolescents 12 to 17 years of age but in different antigen doses.

METHODS: We assessed the real-world effectiveness of the BNT162b2 vaccine against infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) among children and adolescents in Qatar. To compare the incidence of SARS-CoV-2 infection in the national cohort of vaccinated participants with the incidence in the national cohort of unvaccinated participants, we conducted three matched, retrospective, target-trial, cohort studies – one assessing data obtained from children 5 to 11 years of age after the B.1.1.529 (omicron) variant became prevalent and two assessing data from adolescents 12 to 17 years of age before the emergence of the omicron variant (pre-omicron study) and after the omicron variant became prevalent. Associations were estimated with the use of Cox proportional-hazards regression models.

RESULTS: Among children, the overall effectiveness of the 10-μg primary vaccine series against infection with the omicron variant was 25.7% (95% confidence interval [CI], 10.0 to 38.6). Effectiveness was highest (49.6%; 95% CI, 28.5 to 64.5) right after receipt of the second dose but waned rapidly thereafter and was negligible after 3 months. Effectiveness was 46.3% (95% CI, 21.5 to 63.3) among children 5 to 7 years of age and 16.6% (95% CI, -4.2 to 33.2) among those 8 to 11 years of age. Among adolescents, the overall effectiveness of the 30-μg primary vaccine series against infection with the omicron variant was 30.6% (95% CI, 26.9 to 34.1), but many adolescents had been vaccinated months earlier. Effectiveness waned over time since receipt of the second dose. Effectiveness was 35.6% (95% CI, 31.2 to 39.6) among adolescents 12 to 14 years of age and 20.9% (95% CI, 13.8 to 27.4) among those 15 to 17 years of age. In the pre-omicron study, the overall effectiveness of the 30-μg primary vaccine series against SARS-CoV-2 infection among adolescents was 87.6% (95% CI, 84.0 to 90.4) and waned relatively slowly after receipt of the second dose.

CONCLUSIONS: Vaccination in children was associated with modest, rapidly waning protection against omicron infection. Vaccination in adolescents was associated with stronger, more durable protection, perhaps because of the larger antigen dose. (Funded by Weill Cornell Medicine-Qatar and others.).

PMID:36322837 | DOI:10.1056/NEJMoa2210058

J Am Chem Soc. 2022 Nov 2. doi: 10.1021/jacs.2c08770. Online ahead of print.

ABSTRACT

RNA is challenging to target with bioactive small molecules, particularly those of low molecular weight that bind with sufficient affinity and specificity. In this report, we developed a platform to address this challenge, affording a novel bioactive interaction. An RNA-focused small-molecule fragment collection (n = 2500) was constructed by analyzing features in all publicly reported compounds that bind RNA, the largest collection of RNA-focused fragments to date. The RNA-binding landscape for each fragment was studied by using a library-versus-library selection with an RNA library displaying a discrete structural element, probing over 12.8 million interactions, the greatest number of interactions between fragments and biomolecules probed experimentally. Mining of this dataset across the human transcriptome defined a drug-like fragment that potently and specifically targeted the microRNA-372 hairpin precursor, inhibiting its processing into the mature, functional microRNA and alleviating invasive and proliferative oncogenic phenotypes in gastric cancer cells. Importantly, this fragment has favorable properties, including an affinity for the RNA target of 300 ± 130 nM, a molecular weight of 273 Da, and quantitative estimate of drug-likeness (QED) score of 0.8. (For comparison, the mean QED of oral medicines is 0.6 ± 0.2). Thus, these studies demonstrate that a low-molecular weight, fragment-like compound can specifically and potently modulate RNA targets.

PMID:36322830 | DOI:10.1021/jacs.2c08770

Geriatr Psychol Neuropsychiatr Vieil. 2022 Sep 1;20(3):293-302. doi: 10.1684/pnv.2022.1058.

ABSTRACT

INTRODUCTION: Giant cell arteritis (GCA) or Horton’s disease is a segmental and focal inflammation of large and medium-sized arteries mostly seen in patients of 50 years and older. There is also a peak frequency in individuals between the ages of 70 and 80. However, clinical data is scarce in this age group and especially in patients over 80.

METHODS: A retrospective study comprised of patients diagnosed with Horton’s arteritis between 2012 and 2017, according to the American Society of Rheumatology, was conducted at Reims University Hospital. Patients were assigned to two groups according to age (≤ 75 and < 75) in order to evaluate and compare the impact of age on diagnosis, treatment and prognosis.

RESULTS: A total of 67 patients were studied. The mean age upon diagnosis was 75,85 ±8.5 years; 36 patients (53.7%) 75 years or younger and 31 patients older than 75. There was a female predominance (43 patients), 22 patients aged 75 years or younger and 21 older than 75. The mean follow up duration was 43.02 months in patients aged 75 years or younger and 30.99 in patients older than 75. This represents a difference of more than one year in terms of follow up, but is not statistically significant (p = 0.620). Eleven patients (16.4%) died during follow up: 5 patients (13.9%) aged 75 years or younger and 6 patients (19.4%) older than 75 (p = 0.547). Aortitis was significantly less seen in patients older than 75 (p = 0.0410).

CONCLUSION: Our study showed no significant difference in either age group. However, aortitis was less seen in patients older than 75 years. Patients aged 75 or younger seemed more prone to relapses, but their follow up periods were shorter.

PMID:36322811 | DOI:10.1684/pnv.2022.1058